# APSCRIPT

input,s,a,,,,List of input images
output,s,h,"",,,List of output spectra
apertures,s,h,"",,,Apertures
scatter,s,h,"",,,List of scattered light images (optional)
references,s,h,"",,,List of aperture reference images
profiles,s,h,"",,,"List of aperture profile images
"
interactive,b,h,yes,,,Run task interactively?
find,b,h,yes,,,Find apertures?
recenter,b,h,yes,,,Recenter apertures?
resize,b,h,yes,,,Resize apertures?
edit,b,h,yes,,,Edit apertures?
trace,b,h,yes,,,Trace apertures?
fittrace,b,h,yes,,,Fit the traced points interactively?
extract,b,h,yes,,,Extract spectra?
review,b,h,yes,,,Review extractions?
subtract,b,h,yes,,,Subtract scattered light?
smooth,b,h,yes,,,Smooth scattered light along the dispersion?
fitscatter,b,h,yes,,,Fit scattered light interactively?
fitsmooth,b,h,yes,,,"Smooth the scattered light interactively?
"
line,i,h,)params.line,,,>params.line
nsum,i,h,)params.nsum,,,>params.nsum
buffer,r,h,)params.buffer,,,">params.buffer

# OUTPUT PARAMETERS
"
format,s,h,"echelle",,,Extracted spectra format
extras,b,h,)params.extras,,,>params.extras
dbwrite,s,h,"YES",,,Write to database?
initialize,b,h,no,,,Initialize answers?
verbose,b,h,)_.verbose,,,"Verbose output?

# DEFAULT APERTURE PARAMETERS
"
lower,r,h,)params.lower,,,>params.lower
upper,r,h,)params.upper,,,>params.upper
apidtable,s,h,"",,,"Aperture ID table (optional)

# DEFAULT BACKGROUND PARAMETERS
"
b_function,s,h,)params.b_function,,,>params.b_function
b_order,i,h,)params.b_order,,,>params.b_order
b_sample,s,h,)params.b_sample,,,>params.b_sample
b_naverage,i,h,)params.b_naverage,,,>params.b_naverage
b_niterate,i,h,)params.b_niterate,,,>params.b_niterate
b_low_reject,r,h,)params.b_low,,,>params.b_low
b_high_reject,r,h,)params.b_high,,,>params.b_high
b_grow,r,h,)params.b_grow,,,">params.b_grow

# APERTURE CENTERING PARAMETERS
"
width,r,h,,0.,,Profile centering width
radius,r,h,,,,Profile centering radius
threshold,r,h,10.,0.,,"Detection threshold for profile centering

# AUTOMATIC FINDING AND ORDERING PARAMETERS
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nfind,i,h,,,,Number of apertures to be found automatically
minsep,r,h,1.,,,Minimum separation between spectra
maxsep,r,h,100000.,,,Maximum separation between spectra
order,s,h,"increasing","increasing|decreasing",,"Order of apertures

# RECENTERING PARAMETERS
"
aprecenter,s,h,"",,,Apertures for recentering calculation
npeaks,r,h,0.5,,,Select brightest peaks
shift,b,h,yes,,,"Use average shift instead of recentering?

# RESIZING PARAMETERS
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llimit,r,h,INDEF,,,Lower aperture limit relative to center
ulimit,r,h,INDEF,,,Upper aperture limit relative to center
ylevel,r,h,)params.ylevel,,,>params.ylevel
peak,b,h,yes,,,Is ylevel a fraction of the peak?
bkg,b,h,yes,,,"Subtract background in automatic width?"
r_grow,r,h,0.,,,"Grow limits by this factor"
avglimits,b,h,no,,,"Average limits over all apertures?

# EDITING PARAMETERS
"
e_output,s,q,,,,Output spectra rootname
e_profiles,s,q,,,,"Profile reference image

# TRACING PARAMETERS
"
t_nsum,i,h,)params.nsum,,,>params.nsum
t_step,i,h,)params.t_step,,,>params.t_step
t_nlost,i,h,3,1,,Number of consecutive times profile is lost before quitting
t_width,r,h,,0.,,Profile centering width
t_function,s,h,)params.t_function,,,>params.t_function
t_sample,s,h,"*",,,Trace sample regions
t_order,i,h,)params.t_order,,,>params.t_order
t_naverage,i,h,1,,,Trace average or median
t_niterate,i,h,)params.t_niterate,,,>params.t_niterate
t_low_reject,r,h,)params.t_low,,,>params.t_low
t_high_reject,r,h,)params.t_high,,,>params.t_high
t_grow,r,h,0.,0.,,"Trace rejection growing radius

# EXTRACTION PARAMETERS
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background,s,h,,"none|average|median|minimum|fit",,Background to subtract
skybox,i,h,)params.b_smooth,,,>params.b_smooth
weights,s,h,)params.weights,,,>params.weights
pfit,s,h,)params.pfit,,,>params.pfit
clean,b,h,,,,Detect and replace bad pixels?
nclean,r,h,0.5,,,Maximum number of pixels to clean
niterate,i,h,5,0,,Number of profile fitting iterations
saturation,r,h,INDEF,,,Saturation level
readnoise,s,h,,,,Read out noise sigma (photons)
gain,s,h,,,,Photon gain (photons/data number)
lsigma,r,h,)params.lsigma,,,>params.lsigma
usigma,r,h,)params.usigma,,,>params.usigma
polysep,r,h,0.95,0.1,0.95,Marsh algorithm polynomial spacing
polyorder,i,h,10,1,,Marsh algorithm polynomial order
nsubaps,i,h,1,1,,"Number of subapertures per aperture

# ANSWER PARAMETERS
"
ansclobber,s,h,"NO",,," "
ansclobber1,s,h,"NO",,," "
ansdbwrite,s,h,"YES",,," "
ansdbwrite1,s,h,"NO",,," "
ansedit,s,h,"NO",,," "
ansextract,s,h,"NO",,," "
ansfind,s,h,"NO",,," "
ansfit,s,h,"NO",,," "
ansfitscatter,s,h,"NO",,," "
ansfitsmooth,s,h,"NO",,," "
ansfitspec,s,h,"NO",,," "
ansfitspec1,s,h,"NO",,," "
ansfittrace,s,h,"NO",,," "
ansfittrace1,s,h,"NO",,," "
ansflat,s,h,"NO",,," "
ansnorm,s,h,"NO",,," "
ansrecenter,s,h,"NO",,," "
ansresize,s,h,"NO",,," "
ansreview,s,h,"NO",,," "
ansreview1,s,h,"NO",,," "
ansscat,s,h,"NO",,," "
ansskyextract,s,h,"NO",,," "
anssmooth,s,h,"NO",,," "
anstrace,s,h,"NO",,," "